Motivation Intragenic exonic deletions are known to contribute to genetic diseases and are often flanked by regions of homology. Results In order to get a more clear view on these interspersed repeats encompassing a coding sequence, we have developed EDIR (Exome Database of Interspersed Repeats) which contains the positions of these structures within the human exome. EDIR has been calculated by an inductive strategy, rather than by a brute force approach and can be queried through an R/Bioconductor package or a web interface allowing the per gene rapid extraction of homology flanked sequences throughout the exome. Availability The code used to compile EDIR can be found at https://github.com/lauravongoc/EDIR. The full data set of EDIR can be queried via an Rshiny application at http://193.70.34.71:3857/edir/. The R package for querying EDIR is called “EDIRquery” and is available on Bioconductor. The full EDIR data set can be downloaded from https://osf.io/m3gvx/ or http://193.70.34.71/EDIR.tar.gz Supplementary information Supplementary data are available at Bioinformatics online.